Bio::PopGen::Population - A population of individuals
use Bio::PopGen::Population;
use Bio::PopGen::Individual;
my $population = Bio::PopGen::Population->new();
my $ind = Bio::PopGen::Individual->new(-unique_id => 'id');
$population->add_Individual($ind);
for my $ind ( $population->get_Individuals ) {
# iterate through the individuals
}
for my $name ( $population->get_marker_names ) {
my $marker = $population->get_Marker();
}
my $num_inds = $population->get_number_individuals;
my $homozygote_f = $population->get_Frequency_Homozygotes;
my $heterozygote_f = $population->get_Frequency_Heterozygotes;
# make a population haploid by making fake chromosomes through
# haplotypes -- ala allele 1 is on chrom 1 and allele 2 is on chrom 2
# the number of individuals created will thus be 2 x number in
# population
my $happop = $population->haploid_population;
This is a collection of individuals. We'll have ways of generating Bio::PopGen::MarkerI objects out so we can calculate allele_frequencies for implementing the various statistical tests.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $obj = Bio::PopGen::Population->new();
Function: Builds a new Bio::PopGen::Population object
Returns : an instance of Bio::PopGen::Population
Args : -individuals => array ref of individuals (optional)
-name => population name (optional)
-source => a source tag (optional)
-description => a short description string of the population (optional)
Title : name Usage : my $name = $pop->name Function: Get the population name Returns : string representing population name Args : [optional] string representing population name
Title : description Usage : my $description = $pop->description Function: Get the population description Returns : string representing population description Args : [optional] string representing population description
Title : source Usage : my $source = $pop->source Function: Get the population source Returns : string representing population source Args : [optional] string representing population source
Title : annotation Usage : my $annotation_collection = $pop->annotation; Function: Get/set a Bio::AnnotationCollectionI for this population Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object
Title : set_Allele_Frequency
Usage : $population->set_Allele_Frequency('marker' => { 'allele1' => 0.1});
Function: Sets an allele frequency for a Marker for this Population
This allows the Population to not have individual individual
genotypes but rather a set of overall allele frequencies
Returns : Count of the number of markers
Args : -name => (string) marker name
-allele => (string) allele name
-frequency => (double) allele frequency - must be between 0 and 1
OR
-frequencies => { 'marker1' => { 'allele1' => 0.01,
'allele2' => 0.99},
'marker2' => ...
}
Title : add_Individual Usage : $population->add_Individual(@individuals); Function: Add individuals to a population Returns : count of the current number in the object Args : Array of Individuals
Title : remove_Individuals Usage : $population->remove_Individuals(@ids); Function: Remove individual(s) to a population Returns : count of the current number in the object Args : Array of ids
Title : get_Individuals
Usage : my @inds = $pop->get_Individuals();
Function: Return the individuals, alternatively restrict by a criteria
Returns : Array of Bio::PopGen::IndividualI objects
Args : none if want all the individuals OR,
-unique_id => To get an individual with a specific id
-marker => To only get individuals which have a genotype specific
for a specific marker name
Title : get_Genotypes
Usage : my @genotypes = $pop->get_Genotypes(-marker => $name)
Function: Get the genotypes for all the individuals for a specific
marker name
Returns : Array of Bio::PopGen::GenotypeI objects
Args : -marker => name of the marker
Title : get_marker_names Usage : my @names = $pop->get_marker_names; Function: Get the names of the markers Returns : Array of strings Args : [optional] boolean flag to ignore internal cache status
Title : get_Marker Usage : my $marker = $population->get_Marker($name) Function: Get a Bio::PopGen::Marker object based on this population Returns : Bio::PopGen::MarkerI object Args : name of the marker
Title : get_number_individuals Usage : my $count = $pop->get_number_individuals; Function: Get the count of the number of individuals Returns : integer >= 0 Args : none
Title : set_number_individuals
Usage : $pop->set_number_individuals($num);
Function: Fixes the number of individuals, call this with
0 to unset.
Only use this if you know what you are doing,
this is only relavent when you are just adding
allele frequency data for a population and want to
calculate something like theta
Returns : none
Args : individual count, calling it with undef or 0
will reset the value to return a number
calculated from the number of individuals
stored for this population.
Title : get_Frequency_Homozygotes Usage : my $freq = $pop->get_Frequency_Homozygotes; Function: Calculate the frequency of homozygotes in the population Returns : fraction between 0 and 1 Args : $markername
Title : get_Frequency_Heterozygotes Usage : my $freq = $pop->get_Frequency_Homozygotes; Function: Calculate the frequency of homozygotes in the population Returns : fraction between 0 and 1 Args : $markername
Title : haploid_population
Usage : my $pop = $population->haploid_population;
Function: Make a new population where all the individuals
are haploid - effectively an individual out of each
chromosome an individual has.
Returns : L<Bio::PopGen::PopulationI>
Args : None
